Research workbench
Ebov gpdmuc (makona) in complex with rebov-520 and rebov-548 fabs
Analyse Ebov gpdmuc (makona) in complex with rebov-520 and rebov-548 fabs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PCI
- Type
- protein
- Length
- 2,382 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion spike glycoprotein; Rebov-548 Fab heavy chain; Rebov-548 Fab light chain; Virion…
- UniProt
- A0A1C4HDV6, A0A0F6PDW0
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 6 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Virion spike glycoprotein | protein | 225 | 9% helix, 35% strand | A0A1C4HDV6 |
| H, I, J | Rebov-548 Fab heavy chain | protein | 132 | 5% helix, 49% strand | — |
| K, L, M | Rebov-548 Fab light chain | protein | 108 | 3% helix, 47% strand | — |
| D, E, F | Virion spike GLYCOPROTEIN,VIRION spike GLYCOPROTEIN,EBOLA virus (makona) GP2 | protein | 97 | 43% helix, 15% strand | A0A0F6PDW0 |
| Q, R, S | Rebov-520 Fab light chain | protein | 108 | 3% helix, 55% strand | — |
| N, O, P | Rebov-520 Fab heavy chain | protein | 124 | 5% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, D, E, B, F, C, H, L, I, J
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, E, B, F, D, C
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.88 | 0.89 | 113 | empty |
| 2 | 677 | 0.79 | 0.84 | 69 | empty |
| 3 | 106 | 0.78 | 0.98 | 22 | empty |
| 4 | 112 | 0.78 | 0.98 | 22 | empty |
| 5 | 106 | 0.77 | 0.97 | 23 | empty |
Interfaces
39 interfaces between chains.
- B–E · 2446 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 2444 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 2444 Ų buried · 24 hydrogen bonds · protein-protein
- Q–N · 963 Ų buried · 7 hydrogen bonds · protein-protein
- S–P · 963 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6PCI · EBOV GPdMuc (Makona) in complex with rEBOV-520 and rEBOV-548 Fabs · the same entry in another collection · chain N against N, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A1C4HDV6
- Every structure of UniProt A0A0F6PDW0
- Elsewhere: RCSB PDB 6PCI · PDBe 6PCI · UniProt A0A1C4HDV6 · UniProt A0A0F6PDW0
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